It does, if anyone ever uses your code on a server where short tags are disabled. I work with several servers where they are. Other than that though, no. Using the short version makes your script less portable though for the above mentioned reason. This may or may not be an issue for you.
This is another issue entirely, but related. If you are trying to generate certain types of files from PHP (XML is the candidate that comes up most often for me) then having short tags can be an issue. For instance, the following causes a PHP syntax error:
<?xml version="1.0" ?>
You must instead write the following on a server that has short tags enabled:
<?php echo '<?xml version "1.0" ?>'; ?>
Gah!